Bio 98 - Leture 8

Enzymes I

Enzymes1. Selective catalysis and regulation of metabolic rxns - enzymes are unchanged by the reaction - some require co-factors (small organic molecules &/or metals such as Ca, Zn, Cu or Fe, or heme)2. Most are proteins; some RNAs can also catalyze rxns3. Example of extreme catalytic efficiency: “catalase”

Reaction: 2 H2O2 2 H2O + O2

Catalyst Relative rateNone 1Fe3+ 1,000Catalase enzyme (heme) 109 (40,000,000/sec)

3D structure of catalase

Reaction scheme of catalase

Reaction: 2 H2O2 2 H2O + O2

Compound I

Enzymes

4. Another example of extreme catalytic efficiency: “triosephosphate isomerase”

Reaction

Freeenergyprofile

DHAP DAP

3D structure of triosephosphate isomerase (TIM barrel)

The enzyme is so efficient that it is said to be catalytically perfect: It is limited only by the rate the substrate can diffuse into and out of the enzyme’s active site!

3D structure of triosephosphate isomerase (TIM barrel)

Uncatalyzed reaction:

1. G determines where equilibrium lies. 2. G‡ determines the rate at which equilibrium is achieved.

transition statefree energy (activation energy)

overall reactionfree energy changeG

(fr

ee e

nerg

y)

Reaction coordinate

P

S‡

S

(transition state)

G‡

G

S P

1. Enzymes do not alter the equilibrium or G.2. They accelerate reactions by decreasing G‡.3. They accomplish this by stabilizing the transition state(s).

Enzyme-catalyzed reaction:

G (

free

ene

rgy)

Reaction coordinate

E+P

ES‡

E+S G‡

G

S‡

S PE

Models of Enzyme-Substrate Interaction

Emil Fischer, 19th century

Daniel Koshland, 20th century (sequential model for Hb coop.!)

The “Stickase” Enzyme

Factors Contributing to Rate Enhancement by Enzymes1. Concentration - effective molarity in the active site.

2. Orientation - increases the probability of correct bond or orbital alignment.

enzymeA B

A B

k1 (first order rate constant)

Effective molarity = k1[s-1] / k2 [M-1s-1] = k1 / k2 [M]

k2 (second order rate constant)

3. Strain - weakening of bonds by distortion - exemplified by “stickase” model

4. Chemical catalysis (a catch-all term) • major factor for most enzymes • major types: acid-base, covalent, metal ion • a given enzyme may use several types of

chemical catalysis in its mechanism

Combines with the final slide of the lecture

R2

Chymotrypsin is a serine protease that cleaves a peptide at Phe/Tyr/Trp (C) -

leaving a COO- on Phe/Tyr/Trp

2R2

R2

R2

To aid in the understanding of slide 15:Acid-base forms of amino acid side chain